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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease Yunxiao Ren1,2, Ming Hu3,4, Yang E. Li5, Andrew A. Pieper6,7,8,9,10,11, Jeffrey Cummings12 and Feixiong Cheng1,2,4,13 1Cleveland Clinic Genome Center, Cleveland Clinic Research...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...the genotype probabilities of multiple single cells at multiple SNV sites and simultaneously infers the cell lineage tree and genotypes.It is well known that single-cell data are noisy. One of the main sources of noise is allelic dropout (ADO), which is quite common in single-cell data and can lead to fewer...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...noninvasive prenatal screening (NIPS) with an average autosomal sequence depth of ∼0.15×. In studies involving ultra-low coverage sequences, conventional approaches to secure genotype accuracy may fail, especially when multiple samples are pooled. To enhance the proportion of high-quality genotypes in large...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer Gabriela D.A. Guardia1,5, Carlos H. dos Anjos1,5, Aline Rangel-Pozzo2, Filipe F. dos Santos1,3, Alexander Birbrair4, Paula F. Asprino1, Anamaria A. Camargo1 and Pedro A.F. Galante1 1...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
.... A streamlined workflow of enrichment for knockout of multiple genes using V2.1G is provided in Supplemental Figure S7.Drug-resistant surrogate reporters for multigene editingNext, we assessed drug-resistant surrogate reporters in a seven-gene editing experiment MV020. The GFP reporter was fused with Cas9 via F2...
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Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC
- Angela Gomez-Simmonds,
- Medini K. Annavajhala,
- Dwayne Seeram,
- Todd W. Hokunson,
- Heekuk Park,
- and Anne-Catrin Uhlemann
Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
...at a New York City hospital in 1997 (pKm38_N; KY128483), and a blaKPC-encoding plasmid in Salmonella enterica (pAR-0402; CP044187), further corroborating that these plasmids have been circulating for many years in highly diverse hosts (Eilertson et al. 2017; Hazen et al. 2018). Smaller plasmid clusters...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...1 Title 1 Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals 2 conserved gene alterations linked to Parkinson’s disease 3 Running title: Substantia nigra aging linked to Parkinson 4 Kangli Wang1, Weikun Xia1, Yingli Gu1, Songpeng Zu1, Qian Yang2, Maria Luisa Amaral1...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...carcinomas, such as DCIS and LCIS, to invasive forms like IDC. This analysis underscores the potential molecular mechanisms driving breast cancer progression from localized, early-stage lesions to more aggressive, invasive disease.Finally, it is important to note the complexity of tumor tissues, which...
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Method: Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy
- Moonseong Jeong,
- Ali Pazokitoroudi,
- Zhengtong Liu,
- and Sriram Sankararaman
Genome Res. September 2024 34: 1286-1293; Published in Advance July 22, 2024, doi:10.1101/gr.279207.124
...architecture underlying various diseases and traits. Methods that aim to estimate SNP heritability from individual genotype and phenotype data are limited by their ability to scale to Biobank-scale data sets and by the restrictions in access to individual-level data. These limitations have motivated...
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Method: Predicting genotype-specific gene regulatory networks
- Deborah Weighill,
- Marouen Ben Guebila,
- Kimberly Glass,
- John Quackenbush,
- and John Platig
Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
...their individual patterns of gene regulation has the potential to improve our understanding of human health and development, and to refine genotype-specific disease risk assessments and treatments. However, the effects of genetic variants are not typically considered when constructing gene regulatory networks...
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